Variant report

Variant	rs12411254
Chromosome Location	chr1:210674209-210674210
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10735507	0.81[CHD][hapmap]
rs10863839	0.84[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs11582700	0.94[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs12049235	0.84[ASN][1000 genomes]
rs12408469	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12728693	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs12733171	0.92[ASN][1000 genomes]
rs12759944	0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs17188260	0.94[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs2473623	0.89[CHB][hapmap];0.83[CHD][hapmap]
rs4348724	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs4500315	0.94[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4545340	0.81[CHD][hapmap]
rs4622068	0.94[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs4844530	0.86[ASN][1000 genomes]
rs4845035	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4845038	0.91[ASN][1000 genomes]
rs7544655	0.94[CHB][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873147	chr1:210665583-210696806	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv873148	chr1:210665583-210994339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12411254	C1orf186	cis	cerebellum	SCAN
rs12411254	KCNH1	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210653800-210678800	Weak transcription	HSMM	muscle
2	chr1:210670200-210678800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:210672400-210675200	Enhancers	HSMMtube	muscle
4	chr1:210673200-210678800	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:210673600-210675200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:210673600-210679200	Weak transcription	Right Ventricle	heart
7	chr1:210674000-210674400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:210674000-210674400	ZNF genes & repeats	Aorta	Aorta
9	chr1:210674000-210674400	Enhancers	Right Atrium	heart
10	chr1:210674000-210675000	Enhancers	Fetal Heart	heart
11	chr1:210674000-210678400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:210674200-210674600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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